In limma's documentation, the interaction term is described as:
"The first of these questions relates to the WT.S vs WT.U comparison and the second to Mu.S vs Mu.U . The third relates to the difference of differences, i.e., (Mu.S-Mu.U)-(WT.S-WT.U) , which is called the interaction term."
I want to perform the same analysis using DESeq2 (on RNA-seq data).
I have 2 cell types: A and B
for each cell type, I have a KO of a protein and a control (no KO)
I looked at the vignette and at ?results, but I have some doubt regarding what would be equivalent to limma's interaction term (A_ko-A_control)-(B_ko-B_control)
Could someone tell me if the following attempt is correct:
dds <- makeExampleDESeqDataSet(n=100,m=12)
dds$celltype <- factor(c(rep("A",6), rep("B", 6)))
dds$protein <- factor(rep(c(rep("ko",3), rep("control", 3)), 2))
design(dds) <- ~ celltype + protein + celltype:protein
dds <- DESeq(dds)
res <- results(dds, contrast=list( c("protein_ko_vs_control","celltypeB.proteinko") ))
Thanks a lot!